<li>Found a way to get items with null/empty metadata values from SQL</li>
<li>First, find the <code>metadata_field_id</code> for the field you want from the <code>metadatafieldregistry</code> table:</li>
</ul>
<pre><code>dspacetest=# select * from metadatafieldregistry;
</code></pre>
<ul>
<li>In this case our country field is 78</li>
<li>Now find all resources with type 2 (item) that have null/empty values for that field:</li>
</ul>
<pre><code>dspacetest=# select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=78 and (text_value='' OR text_value IS NULL);
</code></pre>
<ul>
<li>Then you can find the handle that owns it from its <code>resource_id</code>:</li>
</ul>
<pre><code>dspacetest=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id = '22678';
</code></pre>
<ul>
<li>It&rsquo;s 25 items so editing in the web UI is annoying, let&rsquo;s try SQL!</li>
</ul>
<pre><code>dspacetest=# delete from metadatavalue where metadata_field_id=78 and text_value='';
DELETE 25
</code></pre>
<ul>
<li>After that perhaps a regular <code>dspace index-discovery</code> (no -b) <em>should</em> suffice&hellip;</li>
<li>Hmm, I indexed, cleared the Cocoon cache, and restarted Tomcat but the 25 &ldquo;|||&rdquo; countries are still there</li>
<li>Maybe I need to do a full re-index&hellip;</li>
<li>Working on cleaning up Abenet&rsquo;s DAGRIS data with OpenRefine</li>
<li>I discovered two really nice functions in OpenRefine: <code>value.trim()</code> and <code>value.escape(&quot;javascript&quot;)</code> which shows whitespace characters like <code>\r\n</code>!</li>
<li>For some reason when you import an Excel file into OpenRefine it exports dates like 1949 to 1949.0 in the CSV</li>
<li>I re-import the resulting CSV and run a GREL on the date issued column: <code>value.replace(&quot;\.0&quot;, &quot;&quot;)</code></li>
<li>I need to start running DSpace in Mac OS X instead of a Linux VM</li>
<li>After building and running a <code>fresh_install</code> I symlinked the webapps into Tomcat&rsquo;s webapps folder:</li>
<li>Add CATALINA_OPTS in <code>/opt/brew/Cellar/tomcat/8.0.30/libexec/bin/setenv.sh</code>, as this script is sourced by the <code>catalina</code> startup script</li>
<li>Whip up some quick CSS to make the button in the submission workflow use the XMLUI theme&rsquo;s brand colors (<a href="https://github.com/ilri/DSpace/issues/154">#154</a>)</li>
<li>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <a href="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></li>
<li>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs&hellip;</li>
<li>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,&quot;&quot;)</code></li>
<li>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</li>
<li>Logs don&rsquo;t always show anything right when it fails, but eventually one of these appears:</li>
</ul>
<pre><code>org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
</code></pre>
<ul>
<li>or</li>
</ul>
<pre><code>Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
</code></pre>
<ul>
<li>Right now DSpace Test&rsquo;s Tomcat heap is set to 1536m and we have quite a bit of free RAM:</li>
</ul>
<pre><code># free -m
total used free shared buffers cached
Mem: 3950 3902 48 9 37 1311
-/+ buffers/cache: 2552 1397
Swap: 255 57 198
</code></pre>
<ul>
<li>So I&rsquo;ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li>
<li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li>
<li>I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.</li>
<li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li>
<li>Change &ldquo;Extension material&rdquo; to &ldquo;Extension Material&rdquo; in input-forms.xml (a mistake that fell through the cracks when we fixed the others in DSpace 4 era)</li>
<li>Work on tweaks and updates for the social sharing icons on item pages: add Delicious and Mendeley (from Academicons), make links open in new windows, and set the icon color to the theme&rsquo;s primary color (<a href="https://github.com/ilri/DSpace/issues/157">#157</a>)</li>
<li>Tweak date-based facets to show more values in drill-down ranges (<a href="https://github.com/ilri/DSpace/issues/162">#162</a>)</li>
<li>Need to remember to clear the Cocoon cache after deployment or else you don&rsquo;t see the new ranges immediately</li>
<li>Set up recipe on IFTTT to tweet new items from the CGSpace Atom feed to my twitter account</li>
<li>Altmetrics&rsquo; support for Handles is kinda weak, so they can&rsquo;t associate our items with DOIs until they are tweeted or blogged, etc first.</li>
<li>Still waiting for my IFTTT recipe to fire, two days later</li>
<li>It looks like the Atom feed on CGSpace hasn&rsquo;t changed in two days, but there have definitely been new items</li>
<li>The RSS feed is nearly as old, but has different old items there</li>
<li>On a hunch I cleared the Cocoon cache and now the feeds are fresh</li>
<li>Looks like there is configuration option related to this, <code>webui.feed.cache.age</code>, which defaults to 48 hours, though I&rsquo;m not sure what relation it has to the Cocoon cache</li>
<li>In any case, we should change this cache to be something more like 6 hours, as we publish new items several times per day.</li>
<li>Work around a CSS issue with long URLs in the item view (<a href="https://github.com/ilri/DSpace/issues/172">#172</a>)</li>
<li>This included the social icon fixes/updates, date-based facet tweaks, reducing the feed cache age, and fixing a layout issue in XMLUI item view when an item had long URLs</li>
<li>Run nginx updates on CGSpace and DSpace Test (<a href="http://mailman.nginx.org/pipermail/nginx/2016-January/049700.html">1.8.1 and 1.9.10, respectively</a>)</li>
<li>Run updates on DSpace Test and reboot for new Linode kernel <code>Linux 4.4.0-x86_64-linode63</code> (first update in months)</li>
<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
</ul>
<pre><code># cd /home/dspacetest.cgiar.org/log
# ls -lh dspace.log.2015-11-18*
-rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
</code></pre>
<ul>
<li>I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper</li>
<li>Need to remember to go check if everything is ok in a few days and then change CGSpace</li>
<li>CGSpace went down again (due to PostgreSQL idle connections of course)</li>
<li>Current database settings for DSpace are <code>db.maxconnections = 30</code> and <code>db.maxidle = 8</code>, yet idle connections are exceeding this:</li>
<li>I restarted PostgreSQL and Tomcat and it&rsquo;s back</li>
<li>On a related note of why CGSpace is so slow, I decided to finally try the <code>pgtune</code> script to tune the postgres settings:</li>
<li>Last week it was an average of 8 seconds&hellip; now this is <sup>1</sup>&frasl;<sub>4</sub> of that</li>
<li>CCAFS noticed that one of their items displays only the Atmire statlets: <a href="https://cgspace.cgiar.org/handle/10568/42445">https://cgspace.cgiar.org/handle/10568/42445</a></li>
<li>Atmire commented that we should raise the JVM heap size by ~500M, so it is now <code>-Xms3584m -Xmx3584m</code></li>
<li>We weren&rsquo;t out of heap yet, but it&rsquo;s probably fair enough that the DSpace 5 upgrade (and new Atmire modules) requires more memory so it&rsquo;s ok</li>
<li>I have reverted all the pgtune tweaks from the other day, as they didn&rsquo;t fix the stability issues, so I&rsquo;d rather not have them introducing more variables into the equation</li>
<li>The PostgreSQL stats from Munin all point to something database-related with the DSpace 5 upgrade around mid–late November</li>
<li>Atmire sent <a href="https://github.com/ilri/DSpace/pull/161">some fixes</a> to DSpace&rsquo;s REST API code that was leaving contexts open (causing the slow performance and database issues)</li>
<li>After deploying the fix to CGSpace the REST API is consistently faster:</li>
<li>Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn&rsquo;t as good, but it&rsquo;s much faster and causes less IO/CPU load</li>
<li>Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot&rsquo;s crawl rate to the &ldquo;Let Google optimize&rdquo; setting</li>
<li>Getting emails from uptimeRobot and uptimeButler that it&rsquo;s down, and Google Webmaster Tools is sending emails that there is an increase in crawl errors</li>
<li>Looks like there are still a bunch of idle PostgreSQL connections:</li>
<li>Troubleshoot the DSpace 5 OAI breakage caused by nginx routing config</li>
<li>The OAI application requests stylesheets and javascript files with the path <code>/oai/static/css</code>, which gets matched here:</li>
</ul>
<pre><code># static assets we can load from the file system directly with nginx
<li>The document root is relative to the xmlui app, so this gets a 404—I&rsquo;m not sure why it doesn&rsquo;t pass to <code>@tomcat</code></li>
<li>Anyways, I can&rsquo;t find any URIs with path <code>/static</code>, and the more important point is to handle all the static theme assets, so we can just remove <code>static</code> from the regex for now (who cares if we can&rsquo;t use nginx to send Etags for OAI CSS!)</li>
<li>Also, I noticed we aren&rsquo;t setting CSP headers on the static assets, because in nginx headers are inherited in child blocks, but if you use <code>add_header</code> in a child block it doesn&rsquo;t inherit the others</li>
<li>We simply need to add <code>include extra-security.conf;</code> to the above location block (but research and test first)</li>
<li>We should add WOFF assets to the list of things to set expires for:</li>
<li>We should also add <code>aspects/Statistics</code> to the location block for static assets (minus <code>static</code> from above):</li>
<li>Need to check <code>/about</code> on CGSpace, as it&rsquo;s blank on my local test server and we might need to add something there</li>
<li>CGSpace has been up and down all day due to PostgreSQL idle connections (current DSpace pool is 90):</li>
<li>I looked closer at the idle connections and saw that many have been idle for hours (current time on server is <code>2015-11-25T20:20:42+0000</code>):</li>
</ul>
<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | less -S
<li>There is a relevant Jira issue about this: <a href="https://jira.duraspace.org/browse/DS-1458">https://jira.duraspace.org/browse/DS-1458</a></li>
<li>It seems there is some sense changing DSpace&rsquo;s default <code>db.maxidle</code> from unlimited (-1) to something like 8 (Tomcat default) or 10 (Confluence default)</li>
<li>Change <code>db.maxidle</code> from -1 to 10, reduce <code>db.maxconnections</code> from 90 to 50, and restart postgres and tomcat7</li>
<li>Also redeploy DSpace Test with a clean sync of CGSpace and mirror these database settings there as well</li>
<li>Also deploy the nginx fixes for the <code>try_files</code> location block as well as the expires block</li>
<li>CGSpace behaving much better since changing <code>db.maxidle</code> yesterday, but still two up/down notices from monitoring this morning (better than 50!)</li>
<li>CCAFS colleagues mentioned that the REST API is very slow, 24 seconds for one item</li>
<li>Not as bad for me, but still unsustainable if you have to get many:</li>
<li>Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace&rsquo;s thirst can ever be quenched</li>
<li>On another note, SUNScholar&rsquo;s notes suggest adjusting some other postgres variables: <a href="http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database">http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database</a></li>
<li>This might help with REST API speed (which I mentioned above and still need to do real tests)</li>
